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8Y18

Cryo-EM structure of SARS-CoV-2 Omicron JN.1 RBD in complex with human ACE2 (local refinement from the spike protein)

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(A)
Angiotensin-converting enzyme 2polymer60369982.61UniProt (Q9BYF1)
Pfam (PF01401)
Homo sapiens (human)ACE-related carboxypeptidase,Angiotensin-converting enzyme homolog,ACEH,Metalloprotease MPROT15
2B
(B)
Spike glycoproteinpolymer1248138697.11UniProt (P0DTC2)
Pfam (PF16451)
Pfam (PF09408)
Pfam (PF19209)
Pfam (PF01601)
Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2)S glycoprotein,E2,Peplomer protein
3C, D
(C, D)
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched586.52In PDB
GlyTouCan (G15407YE)
4E, F, G
(E, F, G)
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched424.43In PDB
GlyTouCan (G42666HT)
5H
(A)
ZINC IONnon-polymer65.41Chemie (ZN)
6I, J, K
(A, B)
2-acetamido-2-deoxy-beta-D-glucopyranosenon-polymer221.23Chemie (NAG)
Sequence modifications
A: 19 - 615 (UniProt: Q9BYF1)
PDBExternal DatabaseDetails
His 616-expression tag
His 617-expression tag
His 618-expression tag
His 619-expression tag
His 620-expression tag
His 621-expression tag
B: 4 - 1208 (UniProt: P0DTC2)
PDBExternal DatabaseDetails
Met 20-insertion
Pro 21Asn 17variant
Phe 23Thr 19variant
Asn 24Thr 20variant
Leu 25Arg 21variant
Ile 26Thr 22variant
Thr 27Gln 23variant
Thr 28Leu 24variant
Thr 29Pro 25variant
Gln 30Pro 26variant
Ser 31Ala 27variant
Leu 54Ser 50variant
-His 69deletion
-Val 70deletion
Phe 129Val 127variant
Asp 144Gly 142variant
-Tyr 144deletion
Ser 158Phe 157variant
Gly 159Arg 158variant
-Asn 211deletion
Ile 212Leu 212variant
Gly 213Val 213variant
Phe 216Leu 216variant
Asn 245His 245variant
Asp 264Ala 264variant
Val 332Ile 332variant
His 339Gly 339variant
Thr 356Lys 356variant
Phe 371Ser 371variant
Pro 373Ser 373variant
Phe 375Ser 375variant
Ala 376Thr 376variant
Lys 403Arg 403variant
Asn 405Asp 405variant
Ser 408Arg 408variant
Asn 417Lys 417variant
Lys 440Asn 440variant
His 445Val 445variant
Ser 446Gly 446variant
Asp 450Asn 450variant
Trp 452Leu 452variant
Ser 455Leu 455variant
Lys 460Asn 460variant
Asn 477Ser 477variant
Lys 478Thr 478variant
Lys 481Asn 481variant
-Val 483deletion
Lys 484Glu 484variant
Pro 486Phe 486variant
Arg 498Gln 498variant
Tyr 501Asn 501variant
His 505Tyr 505variant
Lys 554Glu 554variant
Val 570Ala 570variant
Gly 614Asp 614variant
Ser 621Pro 621variant
Tyr 655His 655variant
Val 670Ile 670variant
Lys 679Asn 679variant
Arg 681Pro 681variant
Lys 764Asn 764variant
Tyr 796Asp 796variant
Pro 817Phe 817engineered mutation
Pro 892Ala 892engineered mutation
Pro 899Ala 899engineered mutation
Phe 939Ser 939variant
Pro 942Ala 942engineered mutation
His 954Gln 954variant
Lys 969Asn 969variant
Pro 986Lys 986engineered mutation
Pro 987Val 987engineered mutation
Leu 1143Pro 1143variant
Gly 1209-expression tag
Gly 1210-expression tag
Gly 1211-expression tag
Ser 1212-expression tag
Gly 1213-expression tag
Tyr 1214-expression tag
Ile 1215-expression tag
Pro 1216-expression tag
Glu 1217-expression tag
Ala 1218-expression tag
Pro 1219-expression tag
Arg 1220-expression tag
Asp 1221-expression tag
Gly 1222-expression tag
Gln 1223-expression tag
Ala 1224-expression tag
Tyr 1225-expression tag
Val 1226-expression tag
Arg 1227-expression tag
Lys 1228-expression tag
Asp 1229-expression tag
Gly 1230-expression tag
Glu 1231-expression tag
Trp 1232-expression tag
Val 1233-expression tag
Leu 1234-expression tag
Leu 1235-expression tag
Ser 1236-expression tag
Thr 1237-expression tag
Phe 1238-expression tag
Leu 1239-expression tag
Gly 1240-expression tag
Gly 1241-expression tag
Gly 1242-expression tag
Ser 1243-expression tag
Ala 1244-expression tag
Trp 1245-expression tag
Ser 1246-expression tag
His 1247-expression tag
Pro 1248-expression tag
Gln 1249-expression tag
Phe 1250-expression tag
Glu 1251-expression tag
Lys 1252-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains2
Total formula weight208679.7
BranchedNumber of molecules5
Total formula weight2446.3
Non-Polymers*Number of molecules4
Total formula weight729.0
All*Total formula weight211855.0
*Water molecules are not included.

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PDB entries from 2024-11-13

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